crossing96/oncoscreening huggingface dataset:
Mutations in SLC29A3, encoding an equilibrative nucleoside transporter ENT3, cause a familial histiocytosis syndrome (Faisalabad histiocytosis) and familial Rosai-Dorfman disease.	The histiocytoses are a heterogeneous group of disorders characterised by an excessive number of histiocytes. In most cases the pathophysiology is unclear and treatment is nonspecific. Faisalabad histiocytosis (FHC) (MIM 602782) has been classed as an autosomal recessively inherited form of histiocytosis with similarities to Rosai-Dorfman disease (RDD) (also known as sinus histiocytosis with massive lymphadenopathy (SHML)). To elucidate the molecular basis of FHC, we performed autozygosity mapping studies in a large consanguineous family and identified a novel locus at chromosome 10q22.1. Mutation analysis of candidate genes within the target interval identified biallelic germline mutations in SLC29A3 in the FHC kindred and in two families reported to have familial RDD. Analysis of SLC29A3 expression during mouse embryogenesis revealed widespread expression by e14.5 with prominent expression in the central nervous system, eye, inner ear, and epithelial tissues including the gastrointestinal tract. SLC29A3 encodes an intracellular equilibrative nucleoside transporter (hENT3) with affinity for adenosine. Recently germline mutations in SLC29A3 were also described in two rare autosomal recessive disorders with overlapping phenotypes: (a) H syndrome (MIM 612391) that is characterised by cutaneous hyperpigmentation and hypertrichosis, hepatomegaly, heart anomalies, hearing loss, and hypogonadism; and (b) PHID (pigmented hypertrichosis with insulin-dependent diabetes mellitus) syndrome. Our findings suggest that a variety of clinical diagnoses (H and PHID syndromes, FHC, and familial RDD) can be included in a new diagnostic category of SLC29A3 spectrum disorder.	bladder
Urothelial carcinoma of the bladder, lipid cell variant: clinicopathologic findings and LOH analysis.	In this report, we present the clinicopathologic features of 27 cases of the lipid cell variant of urothelial bladder carcinoma. This is a rare variant of bladder cancer recognized by the current WHO classification of urologic tumors. The lipid cell component varied from 10% to 50% of the tumor specimen; in 11 cases the lipid cell component composed greater than 30% of the tumor. The architectural pattern of the tumor varied from solid expansile to infiltrative nests. The large epithelial tumor cells had an eccentrically placed nucleus and abundant vacuolated cytoplasm resembling signetring lipoblasts. Mucin stains were negative in all the cases. Typical features of high grade conventional urothelial carcinoma were present in all the cases with micropapillary or plasmacytoid carcinoma in 2 and 1 cases, respectively; extensive squamous or glandular differentiation was present in 2 additional cases. Most neoplastic cells had nuclei of intermediate nuclear grade with occasional nuclear pleomorphism. Immunohistochemical staining showed that the lipid cell component was positive for cytokeratins 7, 20, CAM 5.2, high molecular weight (34ssE12) and AE1/AE3, epithelial membrane antigen, and thrombomodulin; vimentin and S100 protein were negative. The loss of heterozygosity (LOH) analysis was done on 8 cases using 4 polymorphic microsatellite markers (D9S171, D9S177, IFNA, and TP 53); LOH at least in 1 marker was present in 6 cases. The LOH results were the same for lipid variant and conventional urothelial carcinoma. Pathologic stage was Ta (n=1), T1 (=2), T2, at least (n=7), T3a (n=4), T3b (n=8), and T4a (n=5). Electron microcopy analysis based on 2 cases supported lipid content in tumor cells. Follow-up information was available in all the cases, ranging from 6 to 58 months (mean, 28 mo). Sixteen of the patients died of disease at 16 to 58 months (mean, 33 mo) and 8 patients were alive with disease at 8 to 25 months (mean, 22 mo). Another 3 patients died of other causes at 6 to 15 months (mean, 10 mo). In summary, lipid cell urothelial bladder carcinoma is typically associated with advanced stage high-grade urothelial carcinoma, in which the prognosis is poor and clonally related to the concurrent conventional urothelial carcinoma. In limited samples, it may be misdiagnosed as liposarcoma, sarcomatoid carcinoma (carcinosarcoma), or signetring cell carcinoma. Morphologic distinction from other malignant neoplasms with lipid cell phenotype is critical for its clinical management.	bladder
Intravesical mitomycin-C-induced interstitial pneumonia.	An 84-year-old man with no evidence of pre-existing interstitial pneumonia developed fatal interstitial pneumonia and respiratory failure that could only be explained as an adverse effect of intravesical mitomycin C chemotherapy. He had undergone transurethral resection of bladder cancer 3 times, followed by intravesical mitomycin C chemotherapy 1 month later. He had received intravesical mitomycin C chemotherapy every week for 2 months, and he had complained of dyspnea on exertion 5 days before the last intravesical mitomycin C chemotherapy session. Interstitial infiltration was detected in both the upper and lower lobes of the left lung on the day of the last instillation of mitomycin C. Despite discontinuation of mitomycin C and administration of methylprednisolone, his condition deteriorated and he died. Diagnostic evaluation of other causes of pneumonia, including infection and collagen-vascular diseases, was negative. The autopsy demonstrated diffuse alveolar damage in the lung; there were no remarkable findings in other organs. To our knowledge, this is the first pathologically confirmed case of fatal interstitial pneumonia due to intravesical mitomycin C chemotherapy.	bladder
Prognostic significance of survivin-expressing circulating tumour cells in T1G3 bladder cancer.	OBJECTIVE: To evaluate the prognostic significance of survivin in tumour tissues and that of survivin-expressing circulating tumour cells (CTCs) in T1G3 bladder tumours, as the prognosis of T1G3 bladder cancer is highly variable and unpredictable from clinical and pathological prognostic factors. PATIENTS AND METHODS: The study included 54 patients with T1G3 non-muscle-invasive bladder cancer. Additional inclusion criteria were: tumour size <3 cm, absence of carcinoma in situ and multifocality. The planned follow-up was 24 months. Survivin was evaluated by reverse transcription-polymerase chain reaction in tumour tissues. CTCs were isolated from blood by CELLection Dynabeads (Invitrogen, Carlsbad, CA, USA) coated with the monoclonal antibody towards the human epithelial cell adhesion molecule. Cells were lysed and Dynabeads Oligo(dT) was used to capture poly A + mRNA. cDNA was synthesized and analysed for the expression of CD45, CK8 and survivin. The primary endpoint was disease-free survival (DFS); the favourable group at 24 months was defined as that with no clinical evidence of disease; the unfavourable group was that with evidence of recurrent disease or progressive disease. Tumour survivin expression and presence of CTC were correlated with DFS. Multivariate analysis was used to investigate whether the presence of CTC was an independent indicator of DFS. RESULTS: Survivin was found in half of the tumours; patients with survivin-negative tumours had a longer DFS than those with survivin-positive tumours (chi-square, P = 0.029). CTCs were found in 24/54 patients (44%); 92% of CTC expressed survivin. The difference in DFS between CTC-ve and CTC+ve patients was statistically significant (chi-square, P < 0.001). The presence of CTC was an independent prognostic factor for DFS (P < 0.001). CONCLUSION: The presence of CTC is an independent prognostic factor in patients with T1G3 bladder cancer.	bladder
Intractable haematuria: long-term results after selective embolization of the internal iliac arteries.	OBJECTIVE: To determine the feasibility and efficacy of transarterial embolization (TAE) in haemorrhagic urological emergencies, and to assess the perioperative morbidity, effect of timing of intervention on the requirement for blood transfusion, and the long-term follow-up. PATIENTS AND METHODS: Between October 1997 and March 2009, 44 patients (30 men and 14 women; mean age 79 years, range 51-95) with intractable haematuria secondary to advanced pelvic tumour arising from or invading the bladder, underwent internal iliac TAE. Twenty-four patients had transitional carcinoma of the urinary bladder, 12 adenocarcinoma of the prostate, five carcinoma of the uterus, one cancer of the vagina, two carcinoma of the rectum, three carcinoma of the kidney, two simultaneous carcinoma of prostate and bladder, one simultaneous carcinoma of prostate and kidney and one had haemorrhagic cystitis after radiotherapy. RESULTS: TAE of the internal iliac arteries produced initial complete control of bleeding in 36 of the 44 patients (82%). At a mean (range) follow-up of 10.5 (1-97) months TAE there was permanent control of bleeding in 19 (43%) patients. A second TAE session was use in five (11%) patients and it was successful in two of them. There were 24 patients (55%) who required a mean of 4 (1-17) transfusion units before embolization; only 13 (30%) required more blood products after TAE. The mean haematocrit level before and after TAE was 27% and 31% (P < 0001), and the respective haemoglobin level were 8.7 and 10.3 g/dL (P < 0001). During the follow-up there were no major complications related to TAE; minor complications were post-TAE syndrome in 12 (27%) patients, fever (11%), gluteus pain (14%), nausea (2%), and exterior genital oedema (5%). The 6- and 12-month mortality rates were 66% (29 patients) and 18% (eight), respectively. CONCLUSIONS: TAE should be considered as an alternative less-invasive palliative measure and the treatment of choice in these situations. TAE should always be bilateral, the catheter should advance distally to the origin of the superior gluteal artery and the artery embolized with unresorbable particles. Our study confirms the efficacy and safety of TAE in patients with pelvic malignancy, and indicates that this technique should be considered before surgery. The procedure combines the benefits of a minimally invasive approach in decreasing the cost of surgery and operating time, while maintaining low blood loss and analgesia requirement.	bladder
CAG repeats in the androgen receptor gene are shorter in patients with pulmonary, esophageal or bladder carcinoma and longer in women with uterine leiomyoma.	Preferential occurrence of pulmonary, esophageal and bladder carcinomas in males indicate a possible involvement of androgen receptor (AR)-mediated functions. We evaluated the roles of the CAG repeat polymorphism in AR exon 1 in development of these lesions. The exon 1 of AR gene was amplified in samples from 198 male patients with lung carcinoma, 183 with esophageal carcinoma, 95 with bladder carcinoma and 94 males with appendicitis, as a reference group. Mean numbers of the CAG repeat in these 3 cancer groups were determined to be 20.2, 20.0 and 20.0, respectively, all being significantly smaller than that of the reference group (21.1; P<0.05). Samples from 118 female patients with lung carcinoma and 154 females with appendicitis, as a reference group, were examined, with the mean CAG repeat number significantly smaller (19.8) than that of the female reference group (20.7; P<0.01). Samples from 108 patients with uterine leiomyoma were also examined, and their CAG repeat numbers were found to be markedly expanded (23.4; P<0.01). The patients with multiple leiomyomas tend to carry a longer CAG repeat structure, with the mean CAG repeat number longer in the multicentric multiple cases (24.1) compared to that of the unicentric, multinodular cases (22.2) and those with solitary lesions (23.1; P<0.01). These results indicate that a shorter CAG repeat structure may predispose individuals to a higher risk to some male-predominant neoplasms including pulmonary, esophageal and bladder carcinomas and a longer one confers women greater susceptibility to leiomyoma development in the uterus.	bladder
Infrarenal abdominal aortic aneurysm with concomitant urologic malignancy: treatment results in the era of endovascular aneurysm repair.	During diagnostic workup for urologic malignancies, an abdominal aortic aneurysm (AAA) is identified in a proportion of patients. In the era of open AAA repair, these patients presented a surgical dilemma with regard to the sequence of the operations: cancer treatment first or AAA repair first? Previous assessments have concluded that irrespective of the followed strategy, the early and mediumterm mortality from the two operative procedures in this patient category was significant. With the introduction of endovascular aneurysm repair (EVAR), the mortality and morbidity associated with the treatment of both pathologic conditions may be more favorable than with open aneurysm repair. The objective of this study was to assess, in an institutional series of patients receiving EVAR, the early and long-term survival and complication rates in patients with urologic malignancies. In a series of 385 patients receiving EVAR, 14 had a concomitant urologic malignancy: renal cell carcinoma (5 patients), prostate carcinoma (6 patients), and carcinoma of the bladder (3 patients). The first-month mortality was nil. Long-term survival was 80%, 83%, and 67% for the three tumor types, respectively. EVAR offers improved treatment in patients with concomitant AAA and urologic malignancy and should be considered the first choice for these patients.	bladder
Robot-assisted pelvic lymphadenectomy for bladder cancer--where have we reached by 2009.	"OBJECTIVES: To review the current status and role of robot-assisted laparoscopic pelvic lymphadenectomy. To review the need, extent, lymph node yield, oncological feasibility, and outcome of robot-assisted pelvic lymphadenectomy for invasive bladder cancer in patients undergoing a robot-assisted laparoscopic radical cystectomy. METHODS: The National Library of Medicine and the Pub Med were extensively searched for the cases of robot-assisted laparoscopic pelvic lymphadenectomy performed in conjunction with robot-assisted laparoscopic radical cystectomy for bladder cancer using the following keywords: bladder cancer, pelvic lymphadenectomy, cystectomy, laparoscopy, robot, and robot-assisted radical cystectomy. These were reviewed and analyzed (using certain tabulated parameters) to determine the current status of robot-assisted pelvic lymphadenectomy. RESULTS: The search yielded about 12 major published series (278 cases) of ""robot-assisted radical cystectomy with pelvic lymphadenectomy,"" with an overall acceptable mean operating time(s), complication rate, blood loss, and hospital stay. CONCLUSIONS: Robot-assisted laparoscopic pelvic lymphadenectomy in conjunction with robot-assisted laparoscopic radical cystectomy is an oncologically feasible and technically safe procedure with acceptable early operative outcomes that appear to be comparable to those achieved with open/laparoscopic surgery."	bladder
Late recurrence and progression in non-muscle-invasive bladder cancers after 5-year tumor-free periods.	OBJECTIVES: To evaluate the recurrence and progression in patients with non-muscle-invasive bladder tumors who remained tumor-free for at least 5 years, which should assist in the development of schedules of their follow-up evaluations. Non-muscle-invasive bladder tumors that recur or progress at a late time point are not rare. METHODS: Between 1985 and 2002, 814 cases diagnosed with non-muscle-invasive bladder cancer were treated with transurethral resection. Of these 814 cases, 262 patients with no tumor recurrence for more than 5 years were included in the study. The median follow-up interval was 10.0 years. RESULTS: During the follow-up period, 39 tumors (14.9%) showed tumor recurrence. The 5- and 10-year recurrence-free survival rates were 81.6% and 76.0%, respectively. There was no significant difference in tumor recurrence among the low-, intermediate-, and high-risk groups based on the current clinical guideline. Only the use of intravesical mitomycin C was determined to be a significant unfavorable risk factor for late recurrence. Five patients (1.9%) experienced stage progression, 3 of whom did not have metastases at the time of diagnosis of the progression but died because of bladder cancer disease. CONCLUSIONS: After a 5-year tumor-free period, even in the low-risk group, recurrence occurred at a late time point to a degree that was the same as that for the intermediate- and high-risk groups. Finally, some of the high-risk patients experienced late progression with a high degree of malignant behavior, suggesting longer follow-up is needed for each patient.	bladder
[A case of double cancer involving the urachus and the bladder].	A 49-year-old male was referred to our hospital with the chief complaint of gross hematuria. We performed cystoscopy, and found a solid tumor at the dome of the bladder. Sagittal magnetic resonance imaging revealed an extravesical tumor at the position of the urachus. Transurethral resection of bladder tumor was performed. A solid tumor at the dome and two papillary tumors at the right lateral region of the bladder were observed. A pathological examination revealed adenocarcinoma from the solid tumor and urothelial carcinoma from the papillary tumors. Under a diagnosis of double cancer, adenocarcinoma of the urachus and urothelial carcinoma of bladder, we performed a total cystectomy, neobladder and total resection of the urachus.	bladder
[Combination chemotherapy with gemcitabine and paclitaxel in a hemodialysis patient with metastatic urothelial carcinoma].	A 63-year-old man on hemodialysis for chronic renal failure developed a metastatic urothelial carcinoma and was treated with combination chemotherapies. For first line therapy, gemcitabine (GEM) and carboplatin (CBDCA) were given in combination. CBDCA was administered in a target area under the curve of 5.0 mg x min/ml according to the Calvert formula, followed by infusion of GEM at 1,000 mg/m(2), with hemodialysis started 1 hour after the end of CBDCA administration. Treatment-related adverse effects were severe, with grade 4 thrombocytopenia and neutropenia. Following two cycles of that therapy, partial response (PR) was obtained for lung metastasis, while progressive disease (PD) was noted in the liver. For second line therapy, GEM and paclitaxel (PAC) were given in combination. PAC was administered at 110 mg/m(2) before GEM at 1,000 mg/m(2) with hemodialysis given on the interval days. The adverse effect was grade 3 neutropenia, which was considered acceptable. After two cycles of second line therapy, PR was obtained for both lung and liver metastases, and maintained for 6 months. We concluded that GEM/PAC combination therapy is safe and effective for urothelial carcinoma patients undergoing concurrent hemodialysis.	bladder
Bayesian bivariate meta-analysis of diagnostic test studies using integrated nested Laplace approximations.	For bivariate meta-analysis of diagnostic studies, likelihood approaches are very popular. However, they often run into numerical problems with possible non-convergence. In addition, the construction of confidence intervals is controversial. Bayesian methods based on Markov chain Monte Carlo (MCMC) sampling could be used, but are often difficult to implement, and require long running times and diagnostic convergence checks. Recently, a new Bayesian deterministic inference approach for latent Gaussian models using integrated nested Laplace approximations (INLA) has been proposed. With this approach MCMC sampling becomes redundant as the posterior marginal distributions are directly and accurately approximated. By means of a real data set we investigate the influence of the prior information provided and compare the results obtained by INLA, MCMC, and the maximum likelihood procedure SAS PROC NLMIXED. Using a simulation study we further extend the comparison of INLA and SAS PROC NLMIXED by assessing their performance in terms of bias, mean-squared error, coverage probability, and convergence rate. The results indicate that INLA is more stable and gives generally better coverage probabilities for the pooled estimates and less biased estimates of variance parameters. The user-friendliness of INLA is demonstrated by documented R-code.	bladder
Insights on distinct pathways of thiazolidinediones (PPARgamma ligand)-promoted apoptosis in TRAIL-sensitive or -resistant malignant urothelial cells.	Thiazolidinediones, including rosiglitazone and troglitazone, are insulin-sensitizing drugs and high-affinity ligands for the peroxisome proliferator-activated receptor gamma (PPARgamma). Apart from their antidiabetic activity, these molecules possess antitumor properties. We investigated their potential apoptotic effects on RT4 (derived from a well-differentiated Grade I papillary tumor) and T24 (derived from an undifferentiated Grade III carcinoma) bladder cancer cells. Rosiglitazone induced G2/M or G0/G1 phase cell cycle arrest in RT4 and T24 cells, respectively. Only troglitazone triggered apoptosis via extrinsic and intrinsic pathways in both cell lines. Interestingly, rosiglitazone amplified TRAIL-induced apoptosis in TRAIL-sensitive RT4 cells or let TRAIL-resistant T24 cells to respond to TRAIL. Thiazolidinediones acted through PPARgamma activation-independent mechanisms. The underlying mechanisms involved for the first time in cancer cells the upregulation of soluble and/or membrane-bound TRAIL. This was associated with increased cell surface death receptor 5 expression and c-FLIP and survivin downregulation, mediated in part through proteasome-dependent degradation in troglitazone-promoted cell death. Therefore, the combination of rosiglitazone and TRAIL could be clinically relevant as chemopreventive or therapeutic agents for the treatment of TRAIL-resistant high-grade urothelial cancers.	bladder
Comprehensive surgical and chemotherapy treatment for invasive bladder cancer.	"INTRODUCTION: The treatment of transitional cell bladder cancer with muscular invasion remains difficult, due to the numerous patterns of biological behaviour of the disease. There is controversy regarding the application of systemic therapy in invasive bladder carcinoma and the ideal time for the indication of perioperative chemotherapy. This is an overview of systemic therapy in invasive bladder cancer. MATERIALS AND METHODS: Using MEDLINE, we reviewed relevant English and Spanish literature published during the last five years, with ""chemotherapy in bladder cancer"" as keywords. We selected randomised trials, meta-analyses and clinical trials. RESULTS: We obtained 241 articles, 31 of which referred to neoadjuvant and adjuvant chemotherapy in invasive bladder cancer. We classified the articles into three different groups: neoadjuvant, adjuvant and neoadjuvant plus chemotherapy. This information is shown in the tables within the text. CONCLUSIONS: A multidisciplinary approach to the treatment of invasive bladder cancer is essential to guarantee adequate oncological control. Detailed evaluation and proper selection of each patient is fundamental in determining the best moment to start chemotherapy."	bladder